From peter.neelin at gmail.com Sat Oct 3 10:52:44 2015 From: peter.neelin at gmail.com (Peter Neelin) Date: Sat, 3 Oct 2015 10:52:44 -0400 Subject: [MINC-users] mincreshape -dimsize In-Reply-To: References: Message-ID: On Mon, Sep 21, 2015 at 6:59 PM, Andrew Janke wrote: > On 22 September 2015 at 01:41, Robert D. Vincent > wrote: > > Historically, I believe mincreshape really was only meant to resize the > two > > fastest-varying dimensions (xspace and yspace in this case), at least > > according to the man page. > > Correct, the original reason was due to slice scaling IIRC. If Peter > is still lurking he'll know the answer. > I created the image-conversion-variable interface (ICV functions) to allow existing programs (in 1992) to be easily modified to load minc images. These programs (written by various people, most notably Alan) had a very restricted concept of images and they needed to be able to load the more general minc format images so the ICV layer would massage the images into a suitable type, range, size, orientation, etc. The requirement was only for 2D images, but I generalized the capability to support more dimensions if desired. Mincreshape was originally only intended to allow extraction of hyperslabs from a minc volume. However, it occurred to me that it might also be convenient to expose the ICV functionality at the command-line - cheap to implement and useful for data manipulations - so I threw all of those options in as well. This has led to the confusing mess of options and behaviours that I have left to you all. > As you rightly point out, this is not all that amenable to new users! > Indeed! My deepest apologies. Lesson: no new feature is ever cheap, especially when the software has a lifetime approaching 25 years! Peter -- Peter Neelin (peter.neelin at gmail.com) From zijdenbos at gmail.com Mon Oct 12 11:36:31 2015 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Mon, 12 Oct 2015 17:36:31 +0200 Subject: [MINC-users] register and [0-1] float volumes Message-ID: Hi all, In the flurry of recent improvements to Display/register (thank you Bert et al.!), I was wondering if the problem of register not being able to display float volumes with a range [0,1] has been addressed? AFAIC that is the single most annoying issue with register (I am keeping a register 1.3.6. build from 2009 around that still works for such volumes; or I use a wrapper that converts to byte/short on the fly). Thanks, -- Alex From robert.d.vincent at mcgill.ca Mon Oct 12 11:43:32 2015 From: robert.d.vincent at mcgill.ca (Robert D. Vincent) Date: Mon, 12 Oct 2015 11:43:32 -0400 Subject: [MINC-users] register and [0-1] float volumes In-Reply-To: References: Message-ID: Hi Alex, There is a recent commit that should fix this issue. In a nutshell, I made the code recognize volumes that cannot use an integral colour table, and use a full colour mapping instead. On Oct 12, 2015 11:37 AM, "Alex Zijdenbos" wrote: > Hi all, > > In the flurry of recent improvements to Display/register (thank you Bert et > al.!), I was wondering if the problem of register not being able to display > float volumes with a range [0,1] has been addressed? AFAIC that is the > single most annoying issue with register (I am keeping a register 1.3.6. > build from 2009 around that still works for such volumes; or I use a > wrapper that converts to byte/short on the fly). > > Thanks, > > -- Alex > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From zijdenbos at gmail.com Mon Oct 12 12:21:27 2015 From: zijdenbos at gmail.com (Alex Zijdenbos) Date: Mon, 12 Oct 2015 18:21:27 +0200 Subject: [MINC-users] register and [0-1] float volumes In-Reply-To: References: Message-ID: Very cool - thanks!! On Mon, Oct 12, 2015 at 5:43 PM, Robert D. Vincent < robert.d.vincent at mcgill.ca> wrote: > Hi Alex, > > There is a recent commit that should fix this issue. In a nutshell, I made > the code recognize volumes that cannot use an integral colour table, and > use a full colour mapping instead. > On Oct 12, 2015 11:37 AM, "Alex Zijdenbos" wrote: > > > Hi all, > > > > In the flurry of recent improvements to Display/register (thank you Bert > et > > al.!), I was wondering if the problem of register not being able to > display > > float volumes with a range [0,1] has been addressed? AFAIC that is the > > single most annoying issue with register (I am keeping a register 1.3.6. > > build from 2009 around that still works for such volumes; or I use a > > wrapper that converts to byte/short on the fly). > > > > Thanks, > > > > -- Alex > > _______________________________________________ > > MINC-users at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > From andrew at biospective.com Tue Oct 13 16:08:03 2015 From: andrew at biospective.com (Andrew Wood) Date: Tue, 13 Oct 2015 16:08:03 -0400 Subject: [MINC-users] Building the new Display Message-ID: Hi all, I'm having trouble building the development branch of Display. I checkout the minc-toolkit develop branch, and run this: $ mkdir build $ cmake -DCMAKE_BUILD_TYPE:STRING=Release -DMT_BUILD_VISUAL_TOOLS:BOOL=ON .. $ make It gives me the follow error: minc-toolkit/Display/menu/build_menu.c:79:29: error: ?BICGL_F1_KEY? undeclared here (not in a function) minc-toolkit/Display/menu/build_menu.c:80:29: error: ?BICGL_F2_KEY? undeclared here (not in a function) ... minc-toolkit/Display/menu/build_menu.c:89:29: error: ?BICGL_F11_KEY? undeclared here (not in a function) minc-toolkit/Display/menu/build_menu.c:90:29: error: ?BICGL_F12_KEY? undeclared here (not in a function) minc-toolkit/Display/menu/build_menu.c:91:29: error: ?BICGL_PGUP_KEY? undeclared here (not in a function) minc-toolkit/Display/menu/build_menu.c:92:29: error: ?BICGL_PGDN_KEY? undeclared here (not in a function) make[2]: *** [Display/CMakeFiles/Display.dir/menu/build_menu.c.o] Error 1 make[1]: *** [Display/CMakeFiles/Display.dir/all] Error 2 make: *** [all] Error 2 Does anyone have any idea what I'm missing? Thanks, Andrew From robert.d.vincent at mcgill.ca Tue Oct 13 16:11:36 2015 From: robert.d.vincent at mcgill.ca (Robert D. Vincent) Date: Tue, 13 Oct 2015 16:11:36 -0400 Subject: [MINC-users] Building the new Display In-Reply-To: References: Message-ID: You need the newest develop branches of the bicpl and bicgl libraries. -bert On Oct 13, 2015 4:09 PM, "Andrew Wood" wrote: > Hi all, > > I'm having trouble building the development branch of Display. I checkout > the minc-toolkit develop branch, and run this: > > $ mkdir build > $ cmake -DCMAKE_BUILD_TYPE:STRING=Release -DMT_BUILD_VISUAL_TOOLS:BOOL=ON > .. > $ make > > It gives me the follow error: > > minc-toolkit/Display/menu/build_menu.c:79:29: error: ?BICGL_F1_KEY? > undeclared here (not in a function) > minc-toolkit/Display/menu/build_menu.c:80:29: error: ?BICGL_F2_KEY? > undeclared here (not in a function) > ... > minc-toolkit/Display/menu/build_menu.c:89:29: error: ?BICGL_F11_KEY? > undeclared here (not in a function) > minc-toolkit/Display/menu/build_menu.c:90:29: error: ?BICGL_F12_KEY? > undeclared here (not in a function) > minc-toolkit/Display/menu/build_menu.c:91:29: error: ?BICGL_PGUP_KEY? > undeclared here (not in a function) > minc-toolkit/Display/menu/build_menu.c:92:29: error: ?BICGL_PGDN_KEY? > undeclared here (not in a function) > make[2]: *** [Display/CMakeFiles/Display.dir/menu/build_menu.c.o] Error 1 > make[1]: *** [Display/CMakeFiles/Display.dir/all] Error 2 > make: *** [all] Error 2 > > Does anyone have any idea what I'm missing? > > Thanks, > Andrew > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > From pgravel at bic.mni.mcgill.ca Fri Oct 30 12:06:06 2015 From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL) Date: Fri, 30 Oct 2015 12:06:06 -0400 (EDT) Subject: [MINC-users] CIVET lobe_segment: Label names associated with label numbers? In-Reply-To: References: Message-ID: Dear All, Just wondering if anyone would have the label names associated with the label numbers of the segmented brain (from lobe_segment step) output from CIVET. Meny thanks! Paul From vladimir.fonov at gmail.com Fri Oct 30 12:18:36 2015 From: vladimir.fonov at gmail.com (Vladimir S. FONOV) Date: Fri, 30 Oct 2015 12:18:36 -0400 Subject: [MINC-users] CIVET lobe_segment: Label names associated with label numbers? In-Reply-To: References: Message-ID: <5633985C.6010308@gmail.com> Hello, something like that: https://github.com/BIC-MNI/EZminc/blob/master/scripts/lobes_to_volumes.pl#L34 ? On 15-10-30 12:06 PM, Paul GRAVEL wrote: > Dear All, > > Just wondering if anyone would have the label names associated with the > label numbers of the segmented brain (from lobe_segment step) output > from CIVET. > > Meny thanks! > > Paul > > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users -- Best regards, Vladimir S. FONOV ~ vladimir.fonov gmail.com From pgravel at bic.mni.mcgill.ca Fri Oct 30 12:45:55 2015 From: pgravel at bic.mni.mcgill.ca (Paul GRAVEL) Date: Fri, 30 Oct 2015 12:45:55 -0400 (EDT) Subject: [MINC-users] CIVET lobe_segment: Label names associated with label numbers? In-Reply-To: <5633985C.6010308@gmail.com> References: <5633985C.6010308@gmail.com> Message-ID: Many thanks Vlad! On Fri, 30 Oct 2015, Vladimir S. FONOV wrote: > Hello, > > > something like that: > https://github.com/BIC-MNI/EZminc/blob/master/scripts/lobes_to_volumes.pl#L34 > > ? > > On 15-10-30 12:06 PM, Paul GRAVEL wrote: >> Dear All, >> >> Just wondering if anyone would have the label names associated with the >> label numbers of the segmented brain (from lobe_segment step) output >> from CIVET. >> >> Meny thanks! >> >> Paul >> >> _______________________________________________ >> MINC-users at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users > > > -- > Best regards, > > Vladimir S. FONOV ~ vladimir.fonov gmail.com > _______________________________________________ > MINC-users at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users >